GitPlanet

Cheap and reliable Node.js hosting starts at $3/month, and $1/month static HTML hosting

Created with love in Canada, visit hostnodejs.com today

Feel like to post an Ad? Learn Details
All Projects → zotko → xyz2graph

zotko / xyz2graph

Licence: MIT license
Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.

Programming Languages

python
139335 projects - #7 most used programming language

Labels

visualizationatomchemistryplotlyjupyter-notebookmoleculenetworkxchemoinformaticsxyzxyz-readeradjacency-matrixxyz-files3d-plotadjacency-listmolecular-graphcovalent-radiiatomic-coordinatesmolecular-graphsmolecule-visualization

Projects that are alternatives of or similar to xyz2graph

Version3-1
Version 2020 (3.1) of Chem4Word - A Chemistry Add-In for Microsoft Word
Stars: ✭ 14 (-61.11%)
Mutual labels:  chemistry, molecule
MolDQN-pytorch
A PyTorch Implementation of "Optimization of Molecules via Deep Reinforcement Learning".
Stars: ✭ 58 (+61.11%)
Mutual labels:  chemistry, molecule
Thermo
Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)
Stars: ✭ 279 (+675%)
Mutual labels:  chemistry, molecule
GLaDOS
Web Interface for ChEMBL @ EMBL-EBI
Stars: ✭ 28 (-22.22%)
Mutual labels:  chemistry, chemoinformatics
panel-chemistry
🧪📈 🐍. The purpose of the panel-chemistry project is to make it really easy for you to do DATA ANALYSIS and build powerful DATA AND VIZ APPLICATIONS within the domain of Chemistry using using Python and HoloViz Panel.
Stars: ✭ 94 (+161.11%)
Mutual labels:  chemistry, molecule
molassembler
Chemoinformatics toolkit with support for inorganic molecules
Stars: ✭ 18 (-50%)
Mutual labels:  chemistry, chemoinformatics
Kekule.js
A Javascript cheminformatics toolkit.
Stars: ✭ 156 (+333.33%)
Mutual labels:  chemistry, molecule
MolecularGraph.jl
Graph-based molecule modeling toolkit for cheminformatics
Stars: ✭ 144 (+300%)
Mutual labels:  chemistry, molecule
chemprop
Fast and scalable uncertainty quantification for neural molecular property prediction, accelerated optimization, and guided virtual screening.
Stars: ✭ 75 (+108.33%)
Mutual labels:  chemistry, molecule
organic-chemistry-reaction-prediction-using-NMT
organic chemistry reaction prediction using NMT with Attention
Stars: ✭ 30 (-16.67%)
Mutual labels:  chemistry, chemoinformatics
Chemozart
Web-based 3D molecule editor and visualizer with molecular mechanics calculators.
Stars: ✭ 142 (+294.44%)
Mutual labels:  chemistry, molecule
py4chemoinformatics
Python for chemoinformatics
Stars: ✭ 78 (+116.67%)
Mutual labels:  chemistry, chemoinformatics
chembience
A Docker-based, cloudable platform for the development of chemoinformatics-centric web applications and microservices.
Stars: ✭ 41 (+13.89%)
Mutual labels:  chemistry, chemoinformatics
Version3
Version 3 of Chem4Word - A Chemistry Add-In for Microsoft Word
Stars: ✭ 53 (+47.22%)
Mutual labels:  chemistry, molecule
keras-neural-graph-fingerprint
Keras implementation of Neural Graph Fingerprints as proposed by Duvenaud et al., 2015
Stars: ✭ 47 (+30.56%)
Mutual labels:  atom, molecule
ninja-ui-syntax
Beautiful Atom syntax theme inspired by a Dribbble shot.
Stars: ✭ 17 (-52.78%)
Mutual labels:  atom
mddatasetbuilder
A script to build reference datasets for training neural network potentials from given LAMMPS trajectories.
Stars: ✭ 23 (-36.11%)
Mutual labels:  chemistry
Better-Less
Cross-compatible syntax highlighting for Less
Stars: ✭ 13 (-63.89%)
Mutual labels:  atom
meta-extractor
Super simple and fast html page meta data extractor with low memory footprint
Stars: ✭ 38 (+5.56%)
Mutual labels:  atom
love-atom
Smart autocompletion for the LÖVE framework in Atom.
Stars: ✭ 34 (-5.56%)
Mutual labels:  atom
View All Similar Projects ➔

xyz2graph

xyz2graph is a Python package for reading of .xyz files and constructing of molecular graphs from atomic coordinates. The molecular graph can be converted into NetworkX graph or Plotly figure for 3D visualization in a browser window or in a Jupyter notebook.

Requirements

Installation

python -m pip install git+https://github.com/zotko/xyz2graph.git

Usage

from xyz2graph import MolGraph, to_networkx_graph, to_plotly_figure
from plotly.offline import offline

# Create the MolGraph object
mg = MolGraph()

# Read the data from the .xyz file
mg.read_xyz('path/molecule.xyz')

# Create the Plotly figure object
fig = to_plotly_figure(mg)

# Plot the figure
offline.plot(fig)

# Convert the molecular graph to the NetworkX graph
G = to_networkx_graph(mg)

Usage in Jupyter Notebook

from xyz2graph import MolGraph, to_networkx_graph, to_plotly_figure
from plotly.offline import init_notebook_mode, iplot

# Initiate the Plotly notebook mode
init_notebook_mode(connected=True)

# Create the MolGraph object
mg = MolGraph()

# Read the data from the .xyz file
mg.read_xyz('path/molecule.xyz')

# Create the Plotly figure object
fig = to_plotly_figure(mg)

# Plot the figure
iplot(fig)

Example of usage

Note that the project description data, including the texts, logos, images, and/or trademarks, for each open source project belongs to its rightful owner. If you wish to add or remove any projects, please contact us at [email protected].